Merge remote-tracking branch 'upstream/master' into fix-reports

PennLINC · Jul 9, 2024 · 4489dd2 · 4489dd2
2 parents bce775a + 555556c
commit 4489dd2
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Showing 12 changed files with 224 additions and 225 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -4,7 +4,7 @@ orbs:
 
 .dockersetup: &dockersetup
   docker:
-    - image: pennbbl/qsiprep_build:24.4.29
+    - image: pennbbl/qsiprep_build:24.7.1
   working_directory: /src/qsiprep
 
 runinstall: &runinstall

diff --git a/Dockerfile b/Dockerfile
@@ -5,7 +5,7 @@ RUN pip install build
 RUN apt-get update && \
     apt-get install -y --no-install-recommends git
 
-FROM pennbbl/qsiprep_build:24.4.29
+FROM pennbbl/qsiprep_build:24.7.1
 
 # Install qsiprep
 COPY . /src/qsiprep

diff --git a/pyproject.toml b/pyproject.toml
@@ -18,7 +18,7 @@ license = {file = "LICENSE"}
 requires-python = ">=3.10"
 dependencies = [
     'importlib_resources; python_version < "3.11"',
-    "dipy <= 1.5.0",
+    "dipy>=1.8.0,<1.9.0",
     "dmri-amico == 1.5.4",
     "fury",
     "indexed_gzip <= 1.8.7",
@@ -27,13 +27,13 @@ dependencies = [
     "networkx ~= 2.8.8",
     "nibabel <= 5.2.0",
     "nilearn == 0.10.1",
-    "nipype <= 1.8.6",
+    "nipype == 1.8.6",
     "niworkflows >=1.9,<= 1.10",
     "numpy <= 1.26.3",
     "pandas < 2.0.0",
     "psutil <= 5.9.8",
-    "pyAFQ <= 1.3.2",
-    "pybids < 0.16.1",
+    "pyAFQ == 1.3.2",
+    "pybids",
     "pyyaml",
     "scikit-image",
     "scikit-learn <= 1.4.0",

diff --git a/qsiprep/config.py b/qsiprep/config.py
@@ -498,7 +498,7 @@ def init(cls):
                 "stimuli",
                 "sourcedata",
                 "models",
-                re.compile(r"^\."),
+                re.compile(r"\/\.\w+|^\.\w+"),  # hidden files
                 re.compile(r"sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/(beh|func|eeg|ieeg|meg|perf)"),
             ]
             if cls.participant_label and cls.bids_database_dir is None:

diff --git a/qsiprep/data/pipelines/mrtrix_multishell_msmt_pyafq_tractometry.json b/qsiprep/data/pipelines/mrtrix_multishell_msmt_pyafq_tractometry.json
@@ -83,7 +83,7 @@
                 "dist_to_waypoint": "",
                 "rng": "",
                 "return_idx": false,
-                "presegment_bundle_dict": "",
+                "presegment_bundle_dict": null,
                 "presegment_kwargs": "{}",
                 "filter_by_endpoints": true,
                 "dist_to_atlas": 4,
@@ -104,7 +104,7 @@
                 "csd_tau": 0.1,
                 "gtol": 0.01,
                 "brain_mask_definition": "",
-                "bundle_info": "",
+                "bundle_info": null,
                 "reg_template_spec": "mni_T1",
                 "mapping_definition": "",
                 "reg_subject_spec": "power_map",

diff --git a/qsiprep/data/pipelines/pyafq_tractometry.json b/qsiprep/data/pipelines/pyafq_tractometry.json
@@ -47,7 +47,7 @@
                 "dist_to_waypoint": "",
                 "rng": "",
                 "return_idx": false,
-                "presegment_bundle_dict": "",
+                "presegment_bundle_dict": null,
                 "presegment_kwargs": "{}",
                 "filter_by_endpoints": true,
                 "dist_to_atlas": 4,
@@ -68,7 +68,7 @@
                 "csd_tau": 0.1,
                 "gtol": 0.01,
                 "brain_mask_definition": "",
-                "bundle_info": "",
+                "bundle_info": null,
                 "reg_template_spec": "mni_T1",
                 "mapping_definition": "",
                 "reg_subject_spec": "power_map",

diff --git a/qsiprep/tests/data/pyafq_recon_external_trk_outputs.txt b/qsiprep/tests/data/pyafq_recon_external_trk_outputs.txt
diff --git a/qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt b/qsiprep/tests/data/pyafq_recon_full_optional_outputs.txt
@@ -0,0 +1,4 @@
+qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuateviz_dwi.html
+qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuate_tractography.trk
+qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuate_tractography.trk
+qsirecon-PYAFQ/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap/viz_bundles/sub-ABCD_acq-10per000_coordsys-RASMM_trkmethod-probCSD_recogmethod-AFQ_desc-LeftArcuateviz_dwi.html
diff --git a/qsiprep/tests/data/pyafq_recon_full_outputs.txt b/qsiprep/tests/data/pyafq_recon_full_outputs.txt
diff --git a/qsiprep/tests/utils.py b/qsiprep/tests/utils.py
@@ -1,12 +1,12 @@
 """Utility functions for tests."""
 
+import lzma
 import os
 import tarfile
 from glob import glob
 from gzip import GzipFile
 from io import BytesIO
 
-import lzma
 import requests
 from nipype import logging
 
@@ -121,7 +121,9 @@ def check_generated_files(qsiprep_dir, output_list_file, optional_output_list_fi
         if found_not_expected:
             msg += "\nFound but not expected:\n\t"
             msg += "\n\t".join(found_not_expected)
-        raise ValueError(msg)
+
+        if msg:
+            raise ValueError(msg)
 
 
 def reorder_expected_outputs():

diff --git a/qsiprep/utils/sloppy_recon.py b/qsiprep/utils/sloppy_recon.py
@@ -30,7 +30,8 @@ def make_sloppy(spec):
         ("MRTrix3", "global_tractography"): {"niters": 10000},
         ("pyAFQ", "pyafq_tractometry"): {
             "mapping_definition": 'AffMap(affine_kwargs={"level_iters": [10, 10, 10]})',
-            "bundle_info": '["SLF_L", "ARC_L", "CST_L", "CST_R"]',
+            "bundle_info": 'default18_bd()["Left Superior Longitudinal", "Left Arcuate", '
+            '"Left Corticospinal", "Right Corticospinal"]',
             "n_seeds": 10000,
             "random_seeds": True,
             "export": "all_bundles_figure",

diff --git a/qsiprep/workflows/recon/base.py b/qsiprep/workflows/recon/base.py
@@ -240,14 +240,11 @@ def init_single_subject_recon_wf(subject_id):
             (recon_full_inputs[dwi_file], dwi_recon_wfs[dwi_file],
              [(trait, "inputnode." + trait) for trait in recon_workflow_input_fields]),
 
-            (
-                anat_ingress_node if config.workflow.recon_input_pipeline == "qsiprep"
-                else anat_ingress_nodes[dwi_file],
-                dwi_individual_anatomical_wfs[dwi_file], [
-                    (f"outputnode.{trait}", f"inputnode.{trait}")
-                    for trait in anatomical_workflow_outputs
-                ]
-            )
+            (anat_ingress_node if config.workflow.recon_input_pipeline == "qsiprep"
+             else anat_ingress_nodes[dwi_file],
+             dwi_individual_anatomical_wfs[dwi_file],
+             [(f"outputnode.{trait}", f"inputnode.{trait}")
+              for trait in anatomical_workflow_outputs])
         ])  # fmt:skip
 
     # Fill-in datasinks and reportlet datasinks for the anatomical workflow